Assessment of sperm quality and its ability to be using in artificial reproductive techniques has an enormous value today. The use of the flow cytometry method allows multiple sperm attributes to be assessed simultaneously and is an objective, flexible and efficient method for evaluating sperm quality, evaluating 50000 sperm per minute. Despite the fact that flow cytometry is a powerful tool in investigating many qualities of sperm, it cannot be used for assessing those required to fertilize the oocyte, e.g. to penetrate oocytes in-vitro. By using flow cytometry assays researchers should be able to predict fertilizing potential semen samples more accurately as well as evaluating sperm cell membrane integrity and the state of mitochondria and DNA. The above method also facilitates the pre-selection of the sex of offspring in farm animals and minimizes sex-linked genetic diseases in the human population. This is possible due to the volume difference in sperm heads and the biological variations within X- and Y-sperm population. Although the costs of using flow cytometry for routinely evaluating semen samples seem very high, flow cytometry assays are used to solve specific biotechnology problems in animal reproduction and breeding as well as in human medicine.